The lineage_classifications.csv file is maintained by the WA DOH Molecular Epidemiology Program in order to group the lineages for the Sequencing & Variants Report.
Variables include:
| Variable | Definition | Source |
|---|---|---|
| lineage_extracted | SC2 lineage | extracted from lineage_notes.txt from cov-lineages |
| description | description of lineage_extracted | extracted from lineage_notes.txt from cov-lineages |
| status | "Active" or "Withdrawn" | created from "description" column from lineage_notes.txt |
| who_class | Indicates WHO lineage class | created in R code |
| doh_variant_name | Indicates grouping of lineages into parent group used in the DOH Sequencing & Variants Report | created in R code |
| hex_code | Hex code for color of doh_variant_name; follows CDC Nowast colors | created in R code |
| lineage_reporting_group | 1: currently monitored variants; 2: formerly monitored variants; 3: formerly circulating variants, not monitored | created in R code |
| doh_variant_name_tables | Indicates variant name in numerical/pango form for report tables | created in R code |
